Let's set things straight:
1) All the MIDDLE firmwares/patches that you previously installed modify various system files
2) Non of the CFW updates you may have used are aware of the other patches you applied
3) Going from Official Firmware to 3.55KMW seems to be the right thing to do.
I'll repeat myself:
I was on original firmware 3.41.
Updated directly to the fully patched 3.55(kmeaw).
Everything works. No locks, no black screens no permissions problems, no PKG install errors, no in-game update problems, no update troubles.
Those of you who were in such a rush to install GH 3.55, WKK 3.55, WTNG 3.55 - I'm sorry but I simply can't reproduce your steps and the mess you made with your PS3.